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History of gene_fusion

The changes to the source code of this entry in the repository, newest first, each with the differences it made to the entry's files. They are also listed on GitLab.

[entries] New entry: gene_fusion by Tiago de Paula Peixoto 72a849e
diff --git a/entries/gene_fusion/__init__.py b/entries/gene_fusion/__init__.py
new file mode 100644
index 0000000..62e9410
--- /dev/null
+++ b/entries/gene_fusion/__init__.py
@@ -0,0 +1,54 @@
+#! /usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# Copyright (C) 2026 Tiago de Paula Peixoto <tiago@skewed.de>
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Affero General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE.  See the GNU Affero General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Affero General Public License along
+# with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+
+
+from .. import *
+
+
+title = 'Gene fusions in human neoplasia (2006)'
+description = """A network of gene fusions observed in human cancers, from Höglund et al. (2006), as distributed by KONECT (from P. Holme's collection). Each node is a gene, and an undirected edge connects two genes that were observed to fuse (through chromosomal rearrangements) in neoplasia, according to the Mitelman Database of Chromosome Aberrations in Cancer. The data identify the genes only by indices (their names are not included)."""
+tags = ['Biological', 'Genetic', 'Unweighted']
+url = 'http://konect.cc/networks/gene_fusion'
+citation = [('M. Höglund, A. Frigyesi, F. Mitelman, "A gene fusion network in human neoplasia." Oncogene 25(18), 2674-2678 (2006)', 'https://doi.org/10.1038/sj.onc.1209290'),
+            ('J. Kunegis, "KONECT -- The Koblenz Network Collection." Proceedings of the 22nd International Conference on World Wide Web Companion, 1343-1350 (2013)', 'https://doi.org/10.1145/2487788.2488173')]
+icon_hash = None
+upstream_license = None
+upstream_prefix = 'http://konect.cc/files'
+files = [('download.tsv.gene_fusion.tar.bz2', None, 'konect')]
+
+def postprocess(alt, g):
+    pass
+
+def fetch_upstream(force=False):
+    return fetch_upstream_files(__name__.split(".")[-1], upstream_prefix, files,
+                                force)
+
+@cache_network()
+@coerce_props()
+@annotate()
+def parse(alts=None):
+    global files
+    name = __name__.split(".")[-1]
+    for fname, alt, fmt in files:
+        if alts is not None and alt not in alts:
+            continue
+        with open_upstream_file(name, fname, "rb") as f:
+            g = parse_graph([f], fmt, directed=None)
+        postprocess(alt, g)
+        yield alt, g